1Y5L | pdb_00001y5l

The crystal structure of the NarGHI mutant NarI-H66Y

PDB DOI: https://doi.org/10.2210/pdb1Y5L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2004-12-02 Released: 2005-03-08
Deposition Author(s): Bertero, M.G., Rothery, R.A., Boroumand, N., Palak, M., Blasco, F., Ginet, N., Weiner, J.H., Strynadka, N.C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.237 (Depositor), 0.230 (DCC)
R-Value Work:
0.188 (Depositor), 0.182 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A

Bertero, M.G., Rothery, R.A., Boroumand, N., Palak, M., Blasco, F., Ginet, N., Weiner, J.H., Strynadka, N.C.J.

(2005) J Biological Chem 280: 14836-14843

PubMed: 15615728 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M410457200
Primary Citation Related Structures:
1Y4Z, 1Y5I, 1Y5L, 1Y5N

PubMed Abstract:
The crystal structure of Escherichia coli nitrate reductase A (NarGHI) in complex with pentachlorophenol has been determined to 2.0 A of resolution. We have shown that pentachlorophenol is a potent inhibitor of quinol:nitrate oxidoreductase activity and that it also perturbs the EPR spectrum of one of the hemes located in the membrane anchoring subunit (NarI). This new structural information together with site-directed mutagenesis data, biochemical analyses, and molecular modeling provide the first molecular characterization of a quinol binding and oxidation site (Q-site) in NarGHI. A possible proton conduction pathway linked to electron transfer reactions has also been defined, providing fundamental atomic details of ubiquinol oxidation by NarGHI at the bacterial membrane.

Organizational Affiliation

Department of Biochemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Macromolecule Content

Total Structure Weight: 228.85 kDa
Atom Count: 16,150
Modeled Residue Count: 1,964
Deposited Residue Count: 1,983
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 alpha chain	A	1,246	Escherichia coli	Mutation(s): 0 Gene Names: narG EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P09152 (Escherichia coli (strain K12)) Explore P09152 Go to UniProtKB: P09152
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09152
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 beta chain	B	512	Escherichia coli	Mutation(s): 0 Gene Names: narH EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P11349 (Escherichia coli (strain K12)) Explore P11349 Go to UniProtKB: P11349
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11349
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Respiratory nitrate reductase 1 gamma chain	C	225	Escherichia coli	Mutation(s): 2 Gene Names: narI EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P11350 (Escherichia coli (strain K12)) Explore P11350 Go to UniProtKB: P11350
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11350
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MD1 Query on MD1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ IRGDLSAXQOKWLX-XHEYTWMPSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
3PH Query on 3PH Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], J [auth B], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
6MO Query on 6MO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	C	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237 (Depositor), 0.230 (DCC)
R-Value Work: 0.188 (Depositor), 0.182 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.165	α = 90
b = 241.903	β = 90
c = 139.603	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-03-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-03-08
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2019-09-18
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2021-11-10
Changes: Database references, Derived calculations
Version 2.2: 2023-10-25
Changes: Data collection, Refinement description
Version 2.3: 2024-10-30
Changes: Structure summary